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rmes.poisson
Poisson Approximation of Counts of Clumps of Long Words



Description Usage Options Sequence file Output file Example

Description

For each word W, the program rmes.poisson computes the quantities count_p,exp_p,sigma2,stat,rank under the <m>-order Markov chain model using the Poisson approximation. The statistic stat follows the Gaussian distribution N(0,1). A high positive value of the statistic of the number of clumps stat indicates that the word W appears very frequently in clump, on the contrary a high negative value indicates that the word W appears exceptionally in a non-overlapping way.

Usage

rmes.poisson -h
or 
rmes.poisson -o <prefix> 
             -seq DNA-sequence-file
             [-hmin <hmin>] [-hmax <hmax>]
             [-english]
Note: This algorithm does not take into account the phase (or reading frame) and can only fit the model of order 1.

Options

-h
gives only the syntax of the command.
-o <prefix>
<prefix> is the character string that will be used to name the output file. A file named <prefix>.0 is created. Previous file is replaced, if any.
-seq
This option introduces the name of the sequence-file.
-hmin <hmin>
When set, <hmin> corresponds to the minimal length of words to study.
By default, <hmin> is equal to 3.
-hmax <hmax>
When set, <hmax> corresponds to the maximal length of words to study.
By default, <hmax> is equal to the value of <hmin>.
Maximum value: 15.
-english or -eng
When set, the messages are in english.
By default, they are in french.

Sommaire

Example

Computation of the statistics associated with the number of clumps of the 7-words in the lambda genome.
The output file lambda.p.7_1.0 can then be formatted using rmes.format or displayed with the Splus functions. 
rmes.poisson -o lambda.p.7_1 -seq lambda -hmin 7 -m 1

Sommaire